Browsing by Author "Conradie, Louis Timoteus"

Now showing 1 - 1 of 1
  • Thumbnail Image
    Item
    A bioinformatics tool to detect physical gene clusters in functional genomics data
    (Stellenbosch : Stellenbosch University, 2021-03) Conradie, Louis Timoteus; Patterton, Hugh-G.; Stellenbosch University. Faculty of Science. Dept. of Biochemistry.
    ENGLISH ABSTRACT: Many studies have investigated the biological effects of the external environment on the genetic expression of a living cell. This particular study looks at gene clusters that are switched on at a series of discrete time points when Saccharomyces cerevisiae comes out of stationary phase, when the cell is fed a carbon source after a starvation period. To achieve this, Pyxis2 was developed, a bioinformatics tool that is able to detect gene clusters in functional genomics data from any organism. The program detects physical clusters of genes that share a defined functional genomic property, such as transcriptional activity, that may be interpreted in terms of a biological functionality. Pyxis2 provides several options to the user that may be adjusted for appropriate levels of sensitivity. Pyxis2 is available at https://github.com/Louis-Conradie/Pyxis2_classes_2020. Following the identification of gene clusters that are induced during the exit of stationary phase in yeast, the study is extended to also investigate the biological relationship between the identified genes and possible regulatory mechanisms. These mechanisms may include transcriptional activators and co-activators, epigenetic modifications such as histone H3K9ac acetylation, or the effect of the domain wide change of the spatial structure of chromatin. I show that the mega-Dalton transcriptional activation complex SAGA is associated with some of the transcriptionally induced clusters at early times during stationary phase exit, and that acetylation of lysine 9 of histone H3 is not a detectable property of active clusters. I finally show some association between spatial proximity of parts of the genome and cluster gene induction but find this association in cycling cells as opposed to in cells re-engaging passage through the cell-cycle. I finally discuss the implications of my findings in the context of the current literature and identify future avenues of enquiry.